"100% new" means nothing. The rotor could be warped. As for the axle flange still wobbling when the rotor is off, be careful how you view that as it is a cast part that is machined to final finish. What I suggest you do is remove the rotor and put a dial gauge on the machined face of the axle flange and see if you have excessive runout. Some things you mention cause my antenna to go up, namely the "new rotor" part. Why did you replace that to begin with? Was the old rotor difficult to remove so some ******** beat the hub with a hammer? Did you hit something and damage the rotor, which could have damaged the axle? Lots of questions here...A dial gauge is the answer.
Scottly..
The rotor was newly installed several months ago (and with ease, no hammer), cause of heavy vibrations when applying brakes. Already then I could see how the entire wheel wobbled and then no thought was given that the axle could be bent too. Maybe the axle being bent warped the rotor if the rotor was getting too hot. The new rotor was installed and the vibration problems disappeared when applying brakes. Just recently I noted vibrations while driving, both high and low speeds, when accelerating and crusing. Thinking first a tire was improperly balanced. Sometimes the vibrations would become more notable and sometimes you didnt think much of it.
Anyhow, a dial has been used and with the rotor off the hub its still wobbling. primarily in the horizontal direction. So much that you can see it by eye on the right side and only with gauge on the left side. When applying brakes hard you dont feel any vibrations wierdly! But when rotating the wheel by hand you can hear and feel how the brake pads are frequently touching the rotor.
If you stand above the wheel hub, with the rotor off, you can see when the hub is rotating that the hub is pushing out and in. So the axle being bent is beginning to feel like a probable cause. Only I dont understand how it could have been bent, Ive only had the truch for a year, maybe didnt notice the vibrations in the beginning.
Still without pulling out the axle its impossible to say if the bearing is worn.